Magnesium in PDB 6afv: Proton Pyrophosphatase-L555K Mutant
Enzymatic activity of Proton Pyrophosphatase-L555K Mutant
All present enzymatic activity of Proton Pyrophosphatase-L555K Mutant:
3.6.1.1;
Protein crystallography data
The structure of Proton Pyrophosphatase-L555K Mutant, PDB code: 6afv
was solved by
J.-Y.Tsai,
K.-M.Li,
Y.-J.Sun,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
28.06 /
2.70
|
|
Space group
|
C 1 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
221.347,
88.619,
160.955,
90.00,
126.05,
90.00
|
|
R / Rfree (%)
|
19.7 /
23.9
|
Other elements in 6afv:
The structure of Proton Pyrophosphatase-L555K Mutant also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Proton Pyrophosphatase-L555K Mutant
(pdb code 6afv). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the
Proton Pyrophosphatase-L555K Mutant, PDB code: 6afv:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 10 in 6afv
Go back to
Magnesium Binding Sites List in 6afv
Magnesium binding site 1 out
of 10 in the Proton Pyrophosphatase-L555K Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Proton Pyrophosphatase-L555K Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1003
b:51.7
occ:1.00
|
OD2
|
A:ASP257
|
1.9
|
53.2
|
1.0
|
|
O
|
A:HOH1116
|
2.0
|
45.6
|
1.0
|
|
O2
|
A:PO41002
|
2.1
|
53.9
|
1.0
|
|
O
|
A:HOH1113
|
2.4
|
45.9
|
1.0
|
|
OD1
|
A:ASP253
|
2.5
|
54.3
|
1.0
|
|
O
|
A:HOH1118
|
2.8
|
40.9
|
1.0
|
|
CG
|
A:ASP257
|
3.0
|
49.1
|
1.0
|
|
O
|
A:HOH1127
|
3.3
|
43.8
|
1.0
|
|
OD2
|
A:ASP723
|
3.3
|
43.6
|
1.0
|
|
P
|
A:PO41002
|
3.3
|
49.6
|
1.0
|
|
O1
|
A:PO41002
|
3.4
|
53.3
|
1.0
|
|
CG
|
A:ASP253
|
3.5
|
50.5
|
1.0
|
|
MG
|
A:MG1005
|
3.5
|
47.4
|
1.0
|
|
OD1
|
A:ASP257
|
3.6
|
46.6
|
1.0
|
|
OD2
|
A:ASP253
|
3.8
|
50.1
|
1.0
|
|
O
|
A:HOH1111
|
3.8
|
44.3
|
1.0
|
|
OD2
|
A:ASP727
|
4.1
|
47.3
|
1.0
|
|
NZ
|
A:LYS694
|
4.2
|
45.1
|
1.0
|
|
CB
|
A:ASP257
|
4.2
|
46.9
|
1.0
|
|
O3
|
A:PO41002
|
4.2
|
49.3
|
1.0
|
|
O4
|
A:PO41002
|
4.4
|
43.6
|
1.0
|
|
OD1
|
A:ASP727
|
4.4
|
47.9
|
1.0
|
|
CG
|
A:ASP723
|
4.4
|
40.7
|
1.0
|
|
OE1
|
A:GLU268
|
4.6
|
51.1
|
1.0
|
|
O
|
A:ASP253
|
4.7
|
45.5
|
1.0
|
|
CG
|
A:ASP727
|
4.7
|
44.8
|
1.0
|
|
CB
|
A:ASP253
|
4.8
|
47.6
|
1.0
|
|
OD1
|
A:ASP723
|
4.9
|
41.8
|
1.0
|
|
CD
|
A:GLU268
|
5.0
|
52.8
|
1.0
|
|
O
|
A:HOH1158
|
5.0
|
41.8
|
1.0
|
|
Magnesium binding site 2 out
of 10 in 6afv
Go back to
Magnesium Binding Sites List in 6afv
Magnesium binding site 2 out
of 10 in the Proton Pyrophosphatase-L555K Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Proton Pyrophosphatase-L555K Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1004
b:53.4
occ:1.00
|
O
|
A:HOH1152
|
2.1
|
44.9
|
1.0
|
|
O4
|
A:PO41002
|
2.1
|
43.6
|
1.0
|
|
O
|
A:HOH1112
|
2.1
|
55.4
|
1.0
|
|
OD1
|
A:ASP507
|
2.2
|
53.4
|
1.0
|
|
O
|
A:HOH1158
|
2.3
|
41.8
|
1.0
|
|
O
|
A:HOH1141
|
2.3
|
52.7
|
1.0
|
|
OD2
|
A:ASP507
|
2.6
|
47.8
|
1.0
|
|
CG
|
A:ASP507
|
2.7
|
47.2
|
1.0
|
|
O3
|
A:PO41002
|
2.8
|
49.3
|
1.0
|
|
P
|
A:PO41002
|
2.9
|
49.6
|
1.0
|
|
MG
|
A:MG1006
|
3.2
|
52.0
|
1.0
|
|
O2
|
A:PO41002
|
3.4
|
53.9
|
1.0
|
|
O2
|
A:PO41001
|
4.1
|
53.0
|
1.0
|
|
CB
|
A:ASP507
|
4.1
|
43.4
|
1.0
|
|
OD2
|
A:ASP283
|
4.2
|
48.8
|
1.0
|
|
O1
|
A:PO41002
|
4.3
|
53.3
|
1.0
|
|
OD1
|
A:ASP279
|
4.3
|
58.0
|
1.0
|
|
O
|
A:HOH1118
|
4.3
|
40.9
|
1.0
|
|
OD2
|
A:ASP269
|
4.4
|
56.3
|
1.0
|
|
O
|
A:ASP507
|
4.4
|
45.0
|
1.0
|
|
OE2
|
A:GLU268
|
4.6
|
50.2
|
1.0
|
|
OD1
|
A:ASP283
|
4.6
|
48.4
|
1.0
|
|
CA
|
A:ASP507
|
4.7
|
45.9
|
1.0
|
|
OD2
|
A:ASP530
|
4.7
|
54.7
|
1.0
|
|
MG
|
A:MG1007
|
4.7
|
50.0
|
1.0
|
|
OD1
|
A:ASP530
|
4.8
|
52.5
|
1.0
|
|
O
|
A:HOH1132
|
4.8
|
46.1
|
1.0
|
|
C
|
A:ASP507
|
4.8
|
49.8
|
1.0
|
|
CG
|
A:ASP283
|
4.8
|
50.2
|
1.0
|
|
O
|
A:HOH1113
|
4.9
|
45.9
|
1.0
|
|
Magnesium binding site 3 out
of 10 in 6afv
Go back to
Magnesium Binding Sites List in 6afv
Magnesium binding site 3 out
of 10 in the Proton Pyrophosphatase-L555K Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Proton Pyrophosphatase-L555K Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1005
b:47.4
occ:1.00
|
O
|
A:HOH1116
|
1.9
|
45.6
|
1.0
|
|
OD1
|
A:ASP727
|
1.9
|
47.9
|
1.0
|
|
O4
|
A:PO41001
|
2.0
|
45.7
|
1.0
|
|
O
|
A:HOH1111
|
2.2
|
44.3
|
1.0
|
|
O1
|
A:PO41002
|
2.3
|
53.3
|
1.0
|
|
OD2
|
A:ASP253
|
2.6
|
50.1
|
1.0
|
|
CG
|
A:ASP727
|
3.0
|
44.8
|
1.0
|
|
CG
|
A:ASP253
|
3.3
|
50.5
|
1.0
|
|
NZ
|
A:LYS730
|
3.3
|
38.6
|
1.0
|
|
P
|
A:PO41001
|
3.4
|
62.2
|
1.0
|
|
P
|
A:PO41002
|
3.4
|
49.6
|
1.0
|
|
OD2
|
A:ASP727
|
3.5
|
47.3
|
1.0
|
|
MG
|
A:MG1003
|
3.5
|
51.7
|
1.0
|
|
OD1
|
A:ASP253
|
3.6
|
54.3
|
1.0
|
|
O2
|
A:PO41002
|
3.6
|
53.9
|
1.0
|
|
CE
|
A:LYS250
|
3.7
|
39.6
|
1.0
|
|
O3
|
A:PO41001
|
3.8
|
47.6
|
1.0
|
|
NZ
|
A:LYS250
|
3.9
|
37.4
|
1.0
|
|
O4
|
A:PO41002
|
3.9
|
43.6
|
1.0
|
|
CB
|
A:ASP727
|
4.2
|
37.1
|
1.0
|
|
O2
|
A:PO41001
|
4.2
|
53.0
|
1.0
|
|
O1
|
A:PO41001
|
4.4
|
61.8
|
1.0
|
|
CB
|
A:ASP253
|
4.4
|
47.6
|
1.0
|
|
OD1
|
A:ASP723
|
4.4
|
41.8
|
1.0
|
|
OD2
|
A:ASP723
|
4.4
|
43.6
|
1.0
|
|
CE
|
A:LYS730
|
4.5
|
41.6
|
1.0
|
|
MG
|
A:MG1006
|
4.5
|
52.0
|
1.0
|
|
OD2
|
A:ASP731
|
4.6
|
42.7
|
1.0
|
|
CA
|
A:ASP727
|
4.7
|
42.1
|
1.0
|
|
O3
|
A:PO41002
|
4.7
|
49.3
|
1.0
|
|
OD2
|
A:ASP691
|
4.8
|
41.4
|
1.0
|
|
CG
|
A:ASP723
|
4.8
|
40.7
|
1.0
|
|
O
|
A:HOH1143
|
4.9
|
39.4
|
1.0
|
|
Magnesium binding site 4 out
of 10 in 6afv
Go back to
Magnesium Binding Sites List in 6afv
Magnesium binding site 4 out
of 10 in the Proton Pyrophosphatase-L555K Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Proton Pyrophosphatase-L555K Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1006
b:52.0
occ:1.00
|
O
|
A:HOH1112
|
1.9
|
55.4
|
1.0
|
|
O4
|
A:PO41002
|
2.1
|
43.6
|
1.0
|
|
OD1
|
A:ASP283
|
2.4
|
48.4
|
1.0
|
|
O2
|
A:PO41001
|
2.5
|
53.0
|
1.0
|
|
OD2
|
A:ASP507
|
2.8
|
47.8
|
1.0
|
|
OD2
|
A:ASP253
|
3.1
|
50.1
|
1.0
|
|
MG
|
A:MG1004
|
3.2
|
53.4
|
1.0
|
|
CG
|
A:ASP283
|
3.3
|
50.2
|
1.0
|
|
P
|
A:PO41002
|
3.4
|
49.6
|
1.0
|
|
O
|
A:HOH1110
|
3.5
|
42.2
|
1.0
|
|
OD2
|
A:ASP283
|
3.5
|
48.8
|
1.0
|
|
O4
|
A:PO41001
|
3.6
|
45.7
|
1.0
|
|
P
|
A:PO41001
|
3.6
|
62.2
|
1.0
|
|
OD1
|
A:ASP279
|
3.9
|
58.0
|
1.0
|
|
CG
|
A:ASP507
|
3.9
|
47.2
|
1.0
|
|
O2
|
A:PO41002
|
3.9
|
53.9
|
1.0
|
|
NZ
|
A:LYS250
|
4.0
|
37.4
|
1.0
|
|
CG
|
A:ASP253
|
4.1
|
50.5
|
1.0
|
|
O1
|
A:PO41002
|
4.1
|
53.3
|
1.0
|
|
O
|
A:HOH1158
|
4.3
|
41.8
|
1.0
|
|
O
|
A:HOH1136
|
4.4
|
46.3
|
1.0
|
|
OD1
|
A:ASP507
|
4.4
|
53.4
|
1.0
|
|
MG
|
A:MG1005
|
4.5
|
47.4
|
1.0
|
|
CG
|
A:ASP279
|
4.5
|
57.9
|
1.0
|
|
O3
|
A:PO41002
|
4.5
|
49.3
|
1.0
|
|
OD2
|
A:ASP279
|
4.5
|
59.5
|
1.0
|
|
O
|
A:ASP279
|
4.6
|
53.1
|
1.0
|
|
O1
|
A:PO41001
|
4.6
|
61.8
|
1.0
|
|
O3
|
A:PO41001
|
4.6
|
47.6
|
1.0
|
|
O
|
A:HOH1152
|
4.6
|
44.9
|
1.0
|
|
OD1
|
A:ASP253
|
4.7
|
54.3
|
1.0
|
|
CB
|
A:ASP283
|
4.8
|
48.1
|
1.0
|
|
OG1
|
A:THR249
|
5.0
|
46.6
|
1.0
|
|
OD2
|
A:ASP287
|
5.0
|
48.4
|
1.0
|
|
Magnesium binding site 5 out
of 10 in 6afv
Go back to
Magnesium Binding Sites List in 6afv
Magnesium binding site 5 out
of 10 in the Proton Pyrophosphatase-L555K Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Proton Pyrophosphatase-L555K Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1007
b:50.0
occ:1.00
|
O3
|
A:PO41001
|
2.0
|
47.6
|
1.0
|
|
O
|
A:HOH1132
|
2.3
|
46.1
|
1.0
|
|
OD1
|
A:ASN534
|
2.4
|
48.1
|
1.0
|
|
OD2
|
A:ASP691
|
3.0
|
41.4
|
1.0
|
|
P
|
A:PO41001
|
3.2
|
62.2
|
1.0
|
|
O2
|
A:PO41001
|
3.3
|
53.0
|
1.0
|
|
K
|
A:K1008
|
3.3
|
64.8
|
1.0
|
|
O3
|
A:PO41002
|
3.4
|
49.3
|
1.0
|
|
CG
|
A:ASN534
|
3.4
|
48.8
|
1.0
|
|
O1
|
A:PO41002
|
3.6
|
53.3
|
1.0
|
|
OD1
|
A:ASP530
|
3.7
|
52.5
|
1.0
|
|
O
|
A:HOH1176
|
3.7
|
47.3
|
1.0
|
|
O
|
A:HOH1144
|
3.8
|
42.9
|
1.0
|
|
ND2
|
A:ASN534
|
3.8
|
48.1
|
1.0
|
|
P
|
A:PO41002
|
3.8
|
49.6
|
1.0
|
|
OD2
|
A:ASP530
|
3.9
|
54.7
|
1.0
|
|
O
|
A:HOH1136
|
3.9
|
46.3
|
1.0
|
|
O4
|
A:PO41002
|
3.9
|
43.6
|
1.0
|
|
OD1
|
A:ASP507
|
4.0
|
53.4
|
1.0
|
|
CG
|
A:ASP691
|
4.1
|
44.4
|
1.0
|
|
O1
|
A:PO41001
|
4.1
|
61.8
|
1.0
|
|
CG
|
A:ASP530
|
4.1
|
52.3
|
1.0
|
|
OD2
|
A:ASP507
|
4.2
|
47.8
|
1.0
|
|
CG
|
A:ASP507
|
4.2
|
47.2
|
1.0
|
|
O4
|
A:PO41001
|
4.3
|
45.7
|
1.0
|
|
OD1
|
A:ASP691
|
4.4
|
48.4
|
1.0
|
|
O
|
A:ASP530
|
4.5
|
52.8
|
1.0
|
|
MG
|
A:MG1004
|
4.7
|
53.4
|
1.0
|
|
CB
|
A:ASN534
|
4.8
|
45.6
|
1.0
|
|
O
|
A:HOH1111
|
5.0
|
44.3
|
1.0
|
|
Magnesium binding site 6 out
of 10 in 6afv
Go back to
Magnesium Binding Sites List in 6afv
Magnesium binding site 6 out
of 10 in the Proton Pyrophosphatase-L555K Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Proton Pyrophosphatase-L555K Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1003
b:56.5
occ:1.00
|
O
|
B:HOH1128
|
2.1
|
55.5
|
1.0
|
|
O
|
B:HOH1105
|
2.2
|
57.4
|
1.0
|
|
O
|
B:HOH1115
|
2.2
|
51.6
|
1.0
|
|
OD1
|
B:ASP253
|
2.3
|
58.1
|
1.0
|
|
OD2
|
B:ASP257
|
2.4
|
57.1
|
1.0
|
|
O4
|
B:PO41002
|
2.7
|
64.8
|
1.0
|
|
O2
|
B:PO41002
|
2.9
|
53.8
|
1.0
|
|
OD1
|
B:ASP257
|
3.1
|
51.2
|
1.0
|
|
CG
|
B:ASP257
|
3.1
|
49.0
|
1.0
|
|
P
|
B:PO41002
|
3.2
|
53.3
|
1.0
|
|
CG
|
B:ASP253
|
3.3
|
53.4
|
1.0
|
|
OD2
|
B:ASP253
|
3.6
|
53.6
|
1.0
|
|
O3
|
B:PO41002
|
3.6
|
58.8
|
1.0
|
|
MG
|
B:MG1005
|
3.7
|
52.7
|
1.0
|
|
O
|
B:HOH1159
|
3.7
|
60.8
|
1.0
|
|
OD2
|
B:ASP279
|
4.1
|
61.0
|
1.0
|
|
OE1
|
B:GLU268
|
4.2
|
63.5
|
1.0
|
|
CD
|
B:GLU268
|
4.4
|
62.8
|
1.0
|
|
O
|
B:ASP253
|
4.4
|
52.7
|
1.0
|
|
CB
|
B:ASP257
|
4.5
|
47.9
|
1.0
|
|
OD2
|
B:ASP723
|
4.5
|
54.5
|
1.0
|
|
CB
|
B:ASP253
|
4.6
|
50.5
|
1.0
|
|
O1
|
B:PO41002
|
4.6
|
64.5
|
1.0
|
|
MG
|
B:MG1004
|
4.7
|
58.3
|
1.0
|
|
O
|
B:HOH1124
|
4.7
|
51.9
|
1.0
|
|
OE2
|
B:GLU268
|
4.8
|
59.7
|
1.0
|
|
NZ
|
B:LYS694
|
4.8
|
53.1
|
1.0
|
|
CA
|
B:ASP253
|
4.8
|
51.7
|
1.0
|
|
CG
|
B:GLU268
|
4.8
|
61.8
|
1.0
|
|
OD2
|
B:ASP727
|
4.9
|
45.7
|
1.0
|
|
C
|
B:ASP253
|
4.9
|
49.2
|
1.0
|
|
Magnesium binding site 7 out
of 10 in 6afv
Go back to
Magnesium Binding Sites List in 6afv
Magnesium binding site 7 out
of 10 in the Proton Pyrophosphatase-L555K Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Proton Pyrophosphatase-L555K Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1004
b:58.3
occ:1.00
|
O
|
B:HOH1159
|
2.0
|
60.8
|
1.0
|
|
OD1
|
B:ASP507
|
2.0
|
64.6
|
1.0
|
|
O
|
B:HOH1126
|
2.0
|
60.8
|
1.0
|
|
O
|
B:HOH1119
|
2.2
|
61.4
|
1.0
|
|
O3
|
B:PO41002
|
2.6
|
58.8
|
1.0
|
|
O
|
B:HOH1120
|
2.6
|
64.7
|
1.0
|
|
CG
|
B:ASP507
|
2.9
|
58.1
|
1.0
|
|
OD2
|
B:ASP507
|
3.0
|
54.2
|
1.0
|
|
O4
|
B:PO41002
|
3.1
|
64.8
|
1.0
|
|
P
|
B:PO41002
|
3.3
|
53.3
|
1.0
|
|
MG
|
B:MG1006
|
3.8
|
54.2
|
1.0
|
|
O1
|
B:PO41002
|
3.9
|
64.5
|
1.0
|
|
OD1
|
B:ASP279
|
4.0
|
61.2
|
1.0
|
|
OD2
|
B:ASP269
|
4.0
|
65.1
|
1.0
|
|
OE2
|
B:GLU268
|
4.1
|
59.7
|
1.0
|
|
O
|
B:ASP507
|
4.2
|
56.3
|
1.0
|
|
O
|
B:HOH1128
|
4.2
|
55.5
|
1.0
|
|
OD1
|
B:ASP269
|
4.3
|
65.9
|
1.0
|
|
CB
|
B:ASP507
|
4.3
|
58.2
|
1.0
|
|
OD2
|
B:ASP283
|
4.3
|
63.1
|
1.0
|
|
CG
|
B:ASP269
|
4.6
|
65.8
|
1.0
|
|
O4
|
B:PO41001
|
4.6
|
61.2
|
1.0
|
|
O2
|
B:PO41002
|
4.7
|
53.8
|
1.0
|
|
MG
|
B:MG1003
|
4.7
|
56.5
|
1.0
|
|
C
|
B:ASP507
|
4.7
|
60.0
|
1.0
|
|
CA
|
B:ASP507
|
4.8
|
59.2
|
1.0
|
|
CD
|
B:GLU268
|
4.9
|
62.8
|
1.0
|
|
CG
|
B:ASP279
|
4.9
|
66.1
|
1.0
|
|
OD2
|
B:ASP530
|
5.0
|
70.5
|
1.0
|
|
Magnesium binding site 8 out
of 10 in 6afv
Go back to
Magnesium Binding Sites List in 6afv
Magnesium binding site 8 out
of 10 in the Proton Pyrophosphatase-L555K Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Proton Pyrophosphatase-L555K Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1005
b:52.7
occ:1.00
|
O2
|
B:PO41002
|
1.9
|
53.8
|
1.0
|
|
OD1
|
B:ASP727
|
2.0
|
50.5
|
1.0
|
|
OD2
|
B:ASP253
|
2.1
|
53.6
|
1.0
|
|
O
|
B:HOH1124
|
2.1
|
51.9
|
1.0
|
|
O
|
B:HOH1115
|
2.1
|
51.6
|
1.0
|
|
O2
|
B:PO41001
|
2.4
|
57.1
|
1.0
|
|
CG
|
B:ASP727
|
2.9
|
50.9
|
1.0
|
|
CG
|
B:ASP253
|
3.0
|
53.4
|
1.0
|
|
OD2
|
B:ASP727
|
3.2
|
45.7
|
1.0
|
|
OD1
|
B:ASP253
|
3.3
|
58.1
|
1.0
|
|
P
|
B:PO41002
|
3.4
|
53.3
|
1.0
|
|
NZ
|
B:LYS730
|
3.6
|
49.1
|
1.0
|
|
MG
|
B:MG1003
|
3.7
|
56.5
|
1.0
|
|
P
|
B:PO41001
|
3.7
|
72.7
|
1.0
|
|
O3
|
B:PO41001
|
3.9
|
58.6
|
1.0
|
|
O3
|
B:PO41002
|
3.9
|
58.8
|
1.0
|
|
CE
|
B:LYS250
|
4.1
|
43.9
|
1.0
|
|
OD2
|
B:ASP723
|
4.1
|
54.5
|
1.0
|
|
CB
|
B:ASP727
|
4.2
|
51.0
|
1.0
|
|
O1
|
B:PO41002
|
4.3
|
64.5
|
1.0
|
|
CB
|
B:ASP253
|
4.3
|
50.5
|
1.0
|
|
O4
|
B:PO41002
|
4.3
|
64.8
|
1.0
|
|
NZ
|
B:LYS250
|
4.3
|
45.8
|
1.0
|
|
OD1
|
B:ASP723
|
4.4
|
55.3
|
1.0
|
|
O4
|
B:PO41001
|
4.5
|
61.2
|
1.0
|
|
O
|
B:HOH1105
|
4.5
|
57.4
|
1.0
|
|
CG
|
B:ASP723
|
4.6
|
50.5
|
1.0
|
|
MG
|
B:MG1006
|
4.7
|
54.2
|
1.0
|
|
CE
|
B:LYS730
|
4.7
|
46.0
|
1.0
|
|
O1
|
B:PO41001
|
4.7
|
74.2
|
1.0
|
|
CA
|
B:ASP727
|
4.8
|
46.9
|
1.0
|
|
O
|
B:HOH1137
|
4.9
|
41.0
|
1.0
|
|
OD2
|
B:ASP257
|
5.0
|
57.1
|
1.0
|
|
OD2
|
B:ASP731
|
5.0
|
52.1
|
1.0
|
|
Magnesium binding site 9 out
of 10 in 6afv
Go back to
Magnesium Binding Sites List in 6afv
Magnesium binding site 9 out
of 10 in the Proton Pyrophosphatase-L555K Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Proton Pyrophosphatase-L555K Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1006
b:54.2
occ:1.00
|
O
|
B:HOH1120
|
1.9
|
64.7
|
1.0
|
|
OD1
|
B:ASP283
|
2.2
|
66.1
|
1.0
|
|
O3
|
B:PO41002
|
2.3
|
58.8
|
1.0
|
|
O4
|
B:PO41001
|
2.5
|
61.2
|
1.0
|
|
OD2
|
B:ASP507
|
2.7
|
54.2
|
1.0
|
|
CG
|
B:ASP283
|
3.1
|
64.7
|
1.0
|
|
O
|
B:HOH1144
|
3.2
|
54.9
|
1.0
|
|
O2
|
B:PO41001
|
3.3
|
57.1
|
1.0
|
|
O
|
B:HOH1118
|
3.3
|
51.6
|
1.0
|
|
OD2
|
B:ASP283
|
3.4
|
63.1
|
1.0
|
|
P
|
B:PO41001
|
3.4
|
72.7
|
1.0
|
|
P
|
B:PO41002
|
3.7
|
53.3
|
1.0
|
|
OD2
|
B:ASP253
|
3.8
|
53.6
|
1.0
|
|
CG
|
B:ASP507
|
3.8
|
58.1
|
1.0
|
|
MG
|
B:MG1004
|
3.8
|
58.3
|
1.0
|
|
NZ
|
B:LYS250
|
4.0
|
45.8
|
1.0
|
|
O2
|
B:PO41002
|
4.1
|
53.8
|
1.0
|
|
OD1
|
B:ASP279
|
4.2
|
61.2
|
1.0
|
|
O1
|
B:PO41001
|
4.2
|
74.2
|
1.0
|
|
OD1
|
B:ASP507
|
4.3
|
64.6
|
1.0
|
|
O1
|
B:PO41002
|
4.4
|
64.5
|
1.0
|
|
CB
|
B:ASP283
|
4.5
|
58.7
|
1.0
|
|
CG
|
B:ASP253
|
4.5
|
53.4
|
1.0
|
|
O
|
B:ASP279
|
4.5
|
60.5
|
1.0
|
|
O3
|
B:PO41001
|
4.6
|
58.6
|
1.0
|
|
MG
|
B:MG1005
|
4.7
|
52.7
|
1.0
|
|
O4
|
B:PO41002
|
4.7
|
64.8
|
1.0
|
|
CG
|
B:ASP279
|
4.8
|
66.1
|
1.0
|
|
O
|
B:HOH1159
|
4.9
|
60.8
|
1.0
|
|
OG1
|
B:THR249
|
4.9
|
54.6
|
1.0
|
|
OD2
|
B:ASP279
|
4.9
|
61.0
|
1.0
|
|
OD2
|
B:ASP287
|
4.9
|
62.8
|
1.0
|
|
CA
|
B:ASP283
|
5.0
|
57.6
|
1.0
|
|
OD1
|
B:ASP253
|
5.0
|
58.1
|
1.0
|
|
Magnesium binding site 10 out
of 10 in 6afv
Go back to
Magnesium Binding Sites List in 6afv
Magnesium binding site 10 out
of 10 in the Proton Pyrophosphatase-L555K Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Proton Pyrophosphatase-L555K Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1007
b:67.7
occ:1.00
|
OD1
|
B:ASN534
|
2.2
|
68.0
|
1.0
|
|
O1
|
B:PO41002
|
2.3
|
64.5
|
1.0
|
|
O3
|
B:PO41001
|
2.5
|
58.6
|
1.0
|
|
CG
|
B:ASN534
|
3.1
|
65.5
|
1.0
|
|
O4
|
B:PO41001
|
3.1
|
61.2
|
1.0
|
|
OD1
|
B:ASP530
|
3.2
|
69.9
|
1.0
|
|
ND2
|
B:ASN534
|
3.3
|
72.0
|
1.0
|
|
K
|
B:K1008
|
3.3
|
87.0
|
1.0
|
|
P
|
B:PO41001
|
3.4
|
72.7
|
1.0
|
|
OD2
|
B:ASP691
|
3.6
|
55.7
|
1.0
|
|
P
|
B:PO41002
|
3.7
|
53.3
|
1.0
|
|
OD2
|
B:ASP530
|
3.8
|
70.5
|
1.0
|
|
O
|
B:HOH1151
|
3.8
|
50.0
|
1.0
|
|
CG
|
B:ASP530
|
3.8
|
73.2
|
1.0
|
|
O
|
B:HOH1148
|
4.0
|
57.4
|
1.0
|
|
O3
|
B:PO41002
|
4.2
|
58.8
|
1.0
|
|
O1
|
B:PO41001
|
4.3
|
74.2
|
1.0
|
|
CG
|
B:ASP507
|
4.3
|
58.1
|
1.0
|
|
O
|
B:ASP530
|
4.3
|
67.3
|
1.0
|
|
OD2
|
B:ASP507
|
4.4
|
54.2
|
1.0
|
|
O2
|
B:PO41002
|
4.4
|
53.8
|
1.0
|
|
CB
|
B:ASP507
|
4.5
|
58.2
|
1.0
|
|
CB
|
B:ASN534
|
4.5
|
63.1
|
1.0
|
|
O2
|
B:PO41001
|
4.5
|
57.1
|
1.0
|
|
CG
|
B:ASP691
|
4.6
|
54.1
|
1.0
|
|
OD1
|
B:ASP507
|
4.7
|
64.6
|
1.0
|
|
O4
|
B:PO41002
|
4.7
|
64.8
|
1.0
|
|
OD1
|
B:ASP691
|
4.9
|
58.5
|
1.0
|
|
CA
|
B:ASN534
|
4.9
|
63.8
|
1.0
|
|
Reference:
J.Y.Tsai,
K.Z.Tang,
K.M.Li,
B.L.Hsu,
Y.W.Chiang,
A.Goldman,
Y.J.Sun.
Roles of the Hydrophobic Gate and Exit Channel in Vigna Radiata Pyrophosphatase Ion Translocation. J. Mol. Biol. V. 431 1619 2019.
ISSN: ESSN 1089-8638
PubMed: 30878480
DOI: 10.1016/J.JMB.2019.03.009
Page generated: Mon Sep 30 19:06:13 2024
|
